Accessing microbial diversity and heterogeneity in the environment

Access to a wealth of environments and the ability to reconstruct genomes for previously unknown and uncultured lineages has lead to a huge expansion in our understanding of the diversity of life on earth. With this genomic information comes the ability to predict roles for these organisms within global geochemical cycles, identifying new players in these pathways. Working at a contaminated aquifer in Rifle, Colorado, we used genome-resolved metagenomics to examine the microbial communities colonizing sediment and groundwater environments. We leveraged multiple metagenomic samples to examine microbial community heterogeneity, identifying key differences between sediment-associated and planktonic communities. Our work resulted in hundreds of genomes for uncultured microbial lineages, including representatives of many Candidate Phyla. We used previously published genome sequences and over a thousand newly reconstructed genomes to position these Candidate Phyla within the known diversity of life on earth.